A Case of Identity
by Lemony Prescott
Summary: John gets hurt on a case and gets Amnesia. Sherlock decides to leave John to protect him, thinking he did John a deed. But when John heals, he sinks into a deep, dark hole. When John gets some sense knocked into him, he goes on a quest to find out what he's been up to for the past two years. Then he happens to bump into a certain Consulting Criminal •Johnlock•Johniarty•Angst•
1. Introduction

A Case of Identity

Introduction

**Disclaimer-**Not mine

Sherlock Holmes didn't notice that John was missing at first. He didn't notice that there weren't footsteps right behind his own. He didn't notice the heavy breathing from running, or the complaints about how fast Sherlock was going.

That was when he stopped dead in his tracks and turned around.

John wasn't there, nor was the suspected killer either.

Sherlock's mind started to race with possible scenarios about what might have happened to his blogger; he also found that he didn't like them either.

Sherlock started to run back to where he and John started. He would yell John's name desperately as he turned every corner in the dark ally. He didn't see John anywhere. That was where Sherlock started to panic. He wondered if John was hurt, or even alive. He wondered if his dear friend would forgive him for accidently abandoning him, even if he didn't mean to do it intentionally. He wondered if that was what the killer wanted, to have John alone so he can hurt him.

Sherlock ran and ran and ran, not leaving a rock unturned. He just needed to find his John Watson.

Sherlock's heart was beating hard and fast in his chest as he ran down another ally. But instead of finding his blogger, he find's DI Greg Lestrade and a cluster of police officers. Sherlock runs as fast as he can to see if they might have found John, but he didn't see his blond friend anywhere. That's when Greg walked up to him with a worried look on his face.

"What is wrong with you? You look like you've been to hell and back!" Lestrade grinned at his own remark.

Sherlock dismissed it with a stern look. "Where is John? Have you seen him? I need to find him! What happened to him? Have you found Moran? I NEED J -"

"- Wait a second, will ya? What do you mean John's missing? He wasn't with you? And yeah, we have Moran; he is over there," Lestrade pointed at a police car.

Sure enough, there stood a smug looking Moran. Sherlock deduced him instantly.

Moran had a blood stain in his blond hair that isn't his. He had scratches that were bleeding down his arm, meaning that he was in some sort of fight. The wound is still bleeding, so it had to happen recently.

Sherlock ran over to Moran to get a better look, ignoring Greg's angry protests on the way.

His clothing was muddy, so was his face. It had rained earlier, Sherlock knew because he and John were in the cab on their way here when it started to lightly drizzle.

Sherlock couldn't help but notice the knowing smirk on Sebastian Moran's face, like he knew what happened to John.

Sherlock moved so he was right in the blond blokes face.

"What did you do to John?" Sherlock was _growling_.

Sebastian put on his best 'innocent face'.

"I have no idea what you're talking about, freak," Sebastian said with a meaningful smile.

Something inside Sherlock snapped.

He grabbed Sebastian by his dirty collar and held him tight.

"What did you do to him? Where is _HE_?! If you touched a _single_ hair on his perfect bod -"

"- Oi, what do ya think you are doing? Sherlock, step back!" Sherlock was pulled back by Lestrade as the men put Moran in the police car. Sherlock wasn't finished with his threat, so he continued.

"My brother will make sure you _suffer_ in prison. He will also make sure that you _stay_ in prison for the rest of your _miserable_, so called life," Sherlock snarled.

Sebastian's smile never dropped; Sherlock didn't like that.

Sherlock turned on his heels and stormed off to find his John, ignoring Lestrade's complaining.

Sherlock stopped suddenly and turned around.

Every one of Lestrade's police officers were looking at Sherlock.

Good.

"I need everyone here to look for my dear friend, John Watson! He had blond hair, below average height, beautiful, endless blue eyes -"

"- Ok, Sherlock! Less about his _beautiful_ _blue_ _eyes_! Everyone, just go search the area!"

Greg grabbed Sherlock by his upper arm and dragged him over to the 'Just in case' ambulance. Sherlock was latterly shaking in rage and worry for his lost friend.

Greg told the medics something, but Sherlock just tuned them out. He only wanted to hear his voice, not Lestrade's, let alone some stranger.

A tall paramedic wrapped Sherlock's shoulders in an orange shock blanket. Sherlock didn't shrug it off; he really didn't care.

Sherlock wondered where John was, and why Sebastian smiled at him like that. Why? Sherlock didn't know the answer. But he did know that Sebastian had _something_ to do with John's disappearance. So, that meant John must have found Moran, but how did Moran beat John? John is ex-mil-

Of course! Moran was a soldier!

Sherlock didn't notice any limp or disfigurement on his body, so he was dishonorably discharged. Sherlock wanted to know what happened, and what he was doing today. He wondered if he was paid to kill his latest victim, or if he was paid to get caught.

Sherlock froze.

What if he was paid to hurt _his_ John? But Sherlock wanted to know one thing.

Did he _succeed_?

But who is he working for?! Why would his boss want to hurt John? His boss obviously gave Moran a big paycheck, judging by the gold watch on him.

Moran hilled his victim from a distance, so he was a sniper, but why would his boss want to throw away a skilled sniper, possibly because he wanted a new worker? But why would he (obviously, it has to be a he) want to purposely pay Sebastian to hurt John? That was when it all snapped together for Sherlock.

'_I will burn the _heart_ out of you.' _

Sherlock shivered under the blanket. His boss was Moriarty, and Sebastian was his right-hand man. He was the one who had pointed the sniper at him and John at the pool.

But what was it all for? And why would Moriarty throw away his sniper?

_John_.

Sherlock's lines of thoughts were cut off by a medic yelling for help.

_John_.

A rush of officers were carrying a body that matched John's description.

_John_.

Sherlock jumped off the ambulance and rushed to his friend's aid.

John wasn't conscious; not good.

John had a bloody gash on the side of his forehead, right by his temple. There was a lot of dried blood in his once sandy blond hair. He was still bleeding as he shook ever so slightly.

They loaded him on a stretcher, ushering Sherlock out of their way.

Sherlock only had time to murmur 'John', before they closed the doors and left for the hospital.

Greg walked behind Sherlock and put a hand on his shoulder. Sherlock turned to Greg with tears in his eyes.

Greg sighed and put Sherlock in his police car.

"We'll go see John, but I can't guaranty that he will be the same. He might have lost some memory. I just want you to be prepared for the unexpected." Sherlock nodded and put his forehead against the window, just like a child.

**A/N- **Hello dear readers! I hope you enjoyed the first chapter. There will be more surprises to come as we progress with this story. Don't forget to tell me if you like it so far, and wish for more!

Favorite, Follow, and Review!

**What is to come?**

_What will John remember? What will he forget?_

_Why does Moriarty want John?_

_Will Sebastian stay in Jail?_

_Will John be the same 'John Watson'?_

**Stay tuned~**

_Lemony _


	2. Sherlock's Decision

A Case of Identity

Chapter 1

**Disclaimer-**Not mine

_"We'll go see John, but I can't guaranty that he will be the same. He might have lost some memory. I just want you to be prepared for the unexpected." Sherlock nodded and put his forehead against the window, just like a child._

Sherlock was sitting in an uncomfortable chair, sulking. He knew that John getting hurt was his entire fault, no matter how many times he was told different. Ms. Hudson, Greg, Mycroft, Molly, and Mike were waiting for news about John's condition.

Sherlock felt like he had somehow let John down. But he always does, doesn't he? Sherlock remembered back to the many times he had disappointed John.

Once, he had done an experiment in one of John's favorite tea cups, and another time, he ruined John's favorite red pants by "accidently" dropping them in alcohol, draining the pants of their redness.

Sherlock would never forget John's face after the 'incident' was done. John would totally ignore him for the rest of the day. But it's not like he missed out on anything, because Sherlock would pout and mope on the couch till John forgave him. But it was a normal routine… a '_Sherlock and John routine.'_

Sherlock would never admit it, but deep down under that curly head, Sherlock knew he loved John. The way John would smile and brightly acknowledge his presence. The way John would comment on Sherlock's intellect and deductions. Sherlock's never been complemented the way he's been complemented by John. Sure he has been bullied and wrongly judged, but he –

"– John Watson?"

Sherlock stood immediately, losing his train of thoughts.

"Ah, yes, are you friends or family? Well, Mr. Watson is in great hands. We have our best men working on his head. Sorry for the wait, but there was a slight problem."

Mycroft raised an eyebrow, "And what 'slight problem' would that be?"

The doctor looked sheepishly at Mycroft before continuing.

"He has lost a lot of blood and passed out on us a couple times. His head is bleeding; it looks like he may have damaged the tissue protecting his brain. He also has a fracture on the back of his head do to the…" The doctor trailed off because of the dark looks he got from the crowd.

"Do NOT say _his_ name or anything like it in my presence. That _man _will be jailed for the rest of his god-forsaken, miserable life."

Everybody turned to Sherlock with a look of shock written on their pale faces. Sherlock didn't know if he might have said something wrong, but the man who would tell him _'not good' _is currently in the emergency.

Sherlock knew that he couldn't keep hurting John, and he also knew that he should just move on, but he was selfish.

John would _not_ be taken away from him. _Ever_.

Sherlock knew his choices. He could both keep John with him and bear the consequences together or he could leave John, breaking both of their hearts in the process.

…

Sherlock made up his mind, not caring whether he liked it or not.

Sherlock grabbed his coat and scarf and stormed out of the hospital with his head held high, ignoring the others as they called his name.

**Authors Note- **I am VERY sorry for the lateness of this fic. I was busy with my other fics. Follow, Favorite, and review! Tell me if you enjoy this fic!

**Coming soon?**

_Will John wake up?_

_What did Sherlock choose?_

_How will John deal with the news about his health?_

_Will Sherlock regret his conclusion?_

_How will the others react to Sherlock's decision?_

**Stay Tuned**

_Lemony_


	3. Showing Emotions

A Case of Identity

Chapter 3

Disclaimer- Not mine

_Sherlock grabbed his coat and scarf and stormed out of the hospital with his head held high, ignoring the others as they called his name._

John woke up with a groan. He tried to open his eyes, but immediately closed them with another moan from the bright light shining down at him. Tears started to prick into his eyes as he struggled to take a breath with a tube down his throat.

"Please calm down, Dr. Watson! The tube is only there to help you breath. Just let it do its job," a soothing voice to his right. John tilted his head towards the soothing voice.

John passed out shortly after he woke.

~.~.~.~.~.~

When Sherlock stormed out of the hospital, he didn't look back. He knew what he wanted for John, even if it'll rip out his heart in the process.

He then flagged down a cab and told his angrily to head to '221b Baker Street.' Sherlock threw money at the driver and jumped out of the car, slamming the door right behind him. He picked opened the door and soared up the stairs, not bothering to see if Ms. Hudson was in or still at the hospital.

He slammed the door open and sighed, ruffling his curls with his hand. He had mentally prepared himself! He knew this would happen sooner or later.

So why was leaving John so difficult?

Sherlock scoffed and feel back into his black chair, grabbing his violin and lightly plucked the strings.

_Sentiment_.

He, of all people, fell in love with John. Sure, John was smart, reasonably handsome, handy, and rather adorable (even though Sherlock would NEVER admit that), but why did Sherlock have to get fond of him? What made John _different_?

Sherlock still didn't know.

~.~.~.~.~.~

Mycroft didn't like his brother's (idiotic) decision to abandon John; he knew somehow, someway, this will come back to bite him, _hard_.

When John would get better, he will want to know what had happened to him these past two years after being deployed from Afghanistan. And this time, Mycroft really didn't want to be the one to explain to him about his brother's mistake.

So when Mycroft decided to abandon John along with his brother, he didn't think twice. If John knew just how bad the Holmes' brothers screwed with him, he'd be out for blood.

Mycroft knew from the start that John would lose some of his past memories, but he didn't know what he would remember. So Mycroft decided to tell Sherlock about his predictions, no matter how Sherlock would deal with it later.

~.~.~.~.~.~

Ms. Hudson, Molly, Greg, Mycroft, Donavon, and Anderson listened attentively, all sitting in 221b as Sherlock spoke about his situation and decision.

"And that's why each and every one of you will _not_ tell John _anything_. It is crucial that he stays out of Moriarty's twisted game. Moriarty is using John as a pawn to get to me. I will not simply sit back and watch John slowly die away to nothing. I love him too much to do tha–"

Everybody in the room gasped, except for Ms. Hudson, of course.

"Oh, Sherlock! How can you just ignore these wonderful feelings? You just have to tell John–"

"– Tell him what, exactly? Tell him how I abandoned him, like how I swore I would never do again? DO you honestly think he would forgive me after all of that?"

Ms. Hudson paled as she remembered how Sherlock had faked his death. That had been a true test on John. He had been put on suicide watch by her, Mycroft, and Greg, after trying to kill himself and failing.

"No, Sherlock. You listen to me, you big headed baboon! John needs you! What will he have to live for? For all he knows, he is not needed anywhere. He'll have no life, or memory of us!"

Sherlock ran a shaky hand through his dark curls, sighing.

"That's exactly my point! He needs to have a life, a chance to have a wife, hell, even snot-nosed children! He can't h-have that wi-with me…"

Sherlock felt tears of sadness prick into his eyes.

He wanted to be there for John, and to watch him grow grey and wrinkly.

_It's for the best. It's for the best. It's for the best._

"Therefore, if I hear that one of you told John something, anything about his past two years, either me or Mycroft will take…certain measures… to make sure it ceases to happen for a second time. Clear?"

Sherlock wiped away the tears that were silently tracking down his face. He looked up to observe everybody's reaction to his decision.

Ms. Hudson had her head bowed and tears leaking out of the corners of her eyes, ruining her foundation.

Greg and Mycroft were frozen and looking anywhere but Sherlock.

Molly was sitting in John's warm chair, crying softly.

Anderson and Donavon were pale and had frowns on their faces.

Sherlock sighed, and sat back down in his chair, grabbing his violin with a slight frown. He softly started to pluck the strings as he wondered where his choice will lead, and what the outcome would be.

Sherlock's frown deepened.

_He didn't know. _

_**Authors Note- **__I am so VERY sorry for the (uber) late update. Follow, Favorite, and review! Tell me if you enjoyed this chapter! I really will try to do better, but I have no idea where this will lead… Just a fair warning. ;D_

_**Coming soon?**_

_How will John deal with the news about his health?_

_Will Sherlock regret his conclusion?_

_Will Sebastian come back? How?_

_How will Jim make his appearance?_

Stay Tuned~

_Lemony_


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